Field‐grown plants have variable exposure to sunlight as a result of
shifting cloud‐cover, seasonal changes, canopy shading, and other
environmental factors. As a result, they need to have developed a method
for dissipating excess energy obtained from periodic excessive sunlight
exposure. Non‐photochemical quenching (NPQ) dissipates excess energy as
heat, however, the physical and molecular genetic mechanics of NPQ
variation are not understood. In this study, we investigated the genetic
loci involved in NPQ by first growing different Arabidopsis thaliana
accessions in local and seasonal climate conditions, then measured
their NPQ kinetics through development by chlorophyll fluorescence. We
used genome‐wide association studies (GWAS) to identify 15 significant
quantitative trait loci (QTL) for a range of photosynthetic traits,
including a QTL co‐located with known NPQ gene PSBS (AT1G44575). We found there were large alternative regulatory segments between the PSBS
promoter regions of the functional haplotypes and a significant
difference in PsbS protein concentration. These findings parallel
studies in rice showing recurrent regulatory evolution of this gene. The
variation in the PSBS promoter and the changes underlying other
QTLs could give insight to allow manipulations of NPQ in crops to
improve their photosynthetic efficiency and yield.